Zinc in PDB 4ey2: Crystal Structure of Ndm-1 Bound to Hydrolyzed Methicillin

All present enzymatic activity of Crystal Structure of Ndm-1 Bound to Hydrolyzed Methicillin:
3.5.2.6;

The structure of Crystal Structure of Ndm-1 Bound to Hydrolyzed Methicillin, PDB code: 4ey2 was solved by N.C.J.Strynadka, D.T.King, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.43 / 1.17
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.120, 79.360, 133.830, 90.00, 90.00, 90.00
R / Rfree (%)	13 / 15.9

The binding sites of Zinc atom in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Methicillin (pdb code 4ey2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Methicillin, PDB code: 4ey2:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Methicillin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Ndm-1 Bound to Hydrolyzed Methicillin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:5.6 occ:0.90 NE2 A:HIS250 2.0 5.7 1.0 OD2 A:ASP124 2.1 6.3 1.0 N4 A:0RM301 2.1 6.7 1.0 O12 A:0RM301 2.2 7.8 1.0 SG A:CYS208 2.4 5.8 1.0 C11 A:0RM301 2.9 7.8 1.0 CE1 A:HIS250 3.0 6.1 1.0 O A:HOH620 3.0 7.1 1.0 C3 A:0RM301 3.0 7.3 1.0 CD2 A:HIS250 3.0 5.9 1.0 C5 A:0RM301 3.3 7.7 1.0 CG A:ASP124 3.3 5.4 1.0 CB A:CYS208 3.4 5.4 1.0 C10 A:0RM301 3.6 9.2 1.0 OD1 A:ASP124 3.8 6.3 1.0 C2 A:0RM301 3.9 7.9 1.0 ND1 A:HIS250 4.1 6.5 1.0 CG A:HIS250 4.2 6.5 1.0 O13 A:0RM301 4.2 10.1 1.0 CB A:SER249 4.2 6.4 1.0 C9 A:0RM301 4.3 8.1 1.0 O8 A:0RM301 4.4 8.6 1.0 CB A:ASP124 4.5 6.1 1.0 CA A:CYS208 4.5 6.0 1.0 S1 A:0RM301 4.5 8.4 1.0 ZN A:ZN303 4.6 5.8 0.9 OG A:SER249 4.6 6.8 1.0 NE2 A:HIS189 4.9 5.0 1.0 C7 A:0RM301 4.9 8.3 1.0 CE1 A:HIS189 4.9 5.8 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Methicillin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Ndm-1 Bound to Hydrolyzed Methicillin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:5.8 occ:0.90 O A:HOH620 2.0 7.1 1.0 ND1 A:HIS122 2.0 7.0 1.0 NE2 A:HIS189 2.0 5.0 1.0 NE2 A:HIS120 2.1 6.5 1.0 O8 A:0RM301 2.5 8.6 1.0 CE1 A:HIS122 2.9 6.9 1.0 CG A:HIS122 3.0 5.7 1.0 CD2 A:HIS189 3.0 4.8 1.0 CE1 A:HIS189 3.0 5.8 1.0 CE1 A:HIS120 3.1 6.4 1.0 CD2 A:HIS120 3.1 6.3 1.0 C7 A:0RM301 3.3 8.3 1.0 CB A:HIS122 3.4 5.4 1.0 C9 A:0RM301 3.8 8.1 1.0 NE2 A:HIS122 4.1 9.1 1.0 N4 A:0RM301 4.1 6.7 1.0 CD2 A:HIS122 4.1 8.1 1.0 CG A:HIS189 4.2 5.2 1.0 ND1 A:HIS189 4.2 5.5 1.0 ND1 A:HIS120 4.2 6.0 1.0 OG A:0RM301 4.2 8.8 1.0 OD1 A:ASP124 4.2 6.3 1.0 CG A:HIS120 4.2 5.4 1.0 CG2 A:THR190 4.3 7.2 1.0 SG A:CYS208 4.3 5.8 1.0 CB A:CYS208 4.4 5.4 1.0 C5 A:0RM301 4.5 7.7 1.0 ZN A:ZN302 4.6 5.6 0.9 CA A:HIS122 4.8 5.8 1.0 C3 A:0RM301 4.9 7.3 1.0 O A:HOH433 4.9 10.7 1.0 N14 A:0RM301 5.0 7.7 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Methicillin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Ndm-1 Bound to Hydrolyzed Methicillin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:5.7 occ:0.90 ND1 B:HIS122 2.0 5.5 1.0 O B:HOH598 2.0 8.5 1.0 NE2 B:HIS189 2.0 5.7 1.0 NE2 B:HIS120 2.1 6.7 1.0 OG B:0RM301 2.5 8.1 1.0 CE1 B:HIS122 2.9 7.2 1.0 CG B:HIS122 3.0 5.8 1.0 CD2 B:HIS189 3.0 6.0 1.0 CE1 B:HIS120 3.0 7.6 1.0 CE1 B:HIS189 3.0 6.5 1.0 CD2 B:HIS120 3.1 6.5 1.0 C7 B:0RM301 3.3 7.9 1.0 CB B:HIS122 3.4 6.2 1.0 C9 B:0RM301 3.8 6.7 1.0 N4 B:0RM301 4.0 7.3 1.0 NE2 B:HIS122 4.1 8.1 1.0 CD2 B:HIS122 4.1 7.9 1.0 ND1 B:HIS189 4.2 6.0 1.0 CG B:HIS189 4.2 5.3 1.0 ND1 B:HIS120 4.2 6.3 1.0 CG2 B:THR190 4.2 6.8 1.0 O8 B:0RM301 4.2 9.1 1.0 OD1 B:ASP124 4.2 5.9 1.0 CG B:HIS120 4.2 5.5 1.0 SG B:CYS208 4.3 6.3 1.0 CB B:CYS208 4.4 6.1 1.0 C5 B:0RM301 4.5 6.9 1.0 ZN B:ZN303 4.6 5.5 0.9 CA B:HIS122 4.9 5.3 1.0 O B:HOH535 4.9 10.3 1.0 C3 B:0RM301 4.9 7.7 1.0 N14 B:0RM301 5.0 6.3 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Methicillin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Ndm-1 Bound to Hydrolyzed Methicillin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:5.5 occ:0.90 NE2 B:HIS250 2.0 5.4 1.0 OD2 B:ASP124 2.1 6.1 1.0 N4 B:0RM301 2.2 7.3 1.0 O13 B:0RM301 2.2 7.9 1.0 SG B:CYS208 2.4 6.3 1.0 C11 B:0RM301 3.0 7.2 1.0 CE1 B:HIS250 3.0 7.0 1.0 O B:HOH598 3.0 8.5 1.0 CD2 B:HIS250 3.0 7.7 1.0 C3 B:0RM301 3.0 7.7 1.0 CG B:ASP124 3.2 5.8 1.0 C5 B:0RM301 3.3 6.9 1.0 CB B:CYS208 3.4 6.1 1.0 C10 B:0RM301 3.6 8.7 1.0 OD1 B:ASP124 3.8 5.9 1.0 C2 B:0RM301 3.9 6.9 1.0 ND1 B:HIS250 4.1 7.6 1.0 CG B:HIS250 4.2 7.9 1.0 CB B:SER249 4.2 6.8 1.0 O12 B:0RM301 4.2 10.1 1.0 C9 B:0RM301 4.3 6.7 1.0 OG B:0RM301 4.4 8.1 1.0 CA B:CYS208 4.5 6.7 1.0 CB B:ASP124 4.5 6.2 1.0 S1 B:0RM301 4.5 7.9 1.0 ZN B:ZN302 4.6 5.7 0.9 OG B:SER249 4.6 7.2 1.0 C7 B:0RM301 4.8 7.9 1.0 NE2 B:HIS189 4.8 5.7 1.0 CE1 B:HIS189 4.9 6.5 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Methicillin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Ndm-1 Bound to Hydrolyzed Methicillin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn304 b:8.4 occ:0.50 O B:HOH612 2.0 26.0 1.0 OD2 B:ASP223 2.0 10.6 1.0 OE2 B:GLU152 2.4 21.9 1.0 OE1 B:GLU152 2.5 14.8 1.0 CD B:GLU152 2.7 12.1 1.0 CG B:ASP223 2.8 9.8 1.0 OD1 B:ASP223 2.9 13.2 1.0 NE2 B:HIS122 3.9 8.1 1.0 O B:HOH421 4.1 10.1 1.0 CG B:GLU152 4.2 9.2 1.0 CB B:ASP223 4.2 8.7 1.0 O B:HOH474 4.5 19.5 1.0 CD2 B:HIS122 4.6 7.9 1.0 O B:HOH488 4.7 18.4 1.0 CE1 B:HIS122 5.0 7.2 1.0

D.T.King, L.J.Worrall, R.Gruninger, N.C.Strynadka. New Delhi Metallo-Beta-Lactamase: Structural Insights Into Beta-Lactam Recognition and Inhibition J.Am.Chem.Soc. V. 134 11362 2012.
ISSN: ISSN 0002-7863
PubMed: 22713171
DOI: 10.1021/JA303579D